Patterns of genetic differentiation among taxa at early stages of divergence provide an opportunity to make inferences about the history of speciation. Here, we conduct a survey of DNA-sequence polymorphism and divergence at loci on the autosomes, X chromosome, Y chromosome and mitochondrial DNA in samples of Mus domesticus, M. musculus and M. castaneus. We analyzed our data under a divergence with gene flow model and estimate that the effective population size of M. castaneus is 200 000–400 000, of M. domesticus is 100 000–200 000 and of M. musculus is 60 000–120 000. These data also suggest that these species started to diverge approximately 500 000 years ago. Consistent with this recent divergence, we observed considerable variation in the genealogical patterns among loci. For some loci, all alleles within each species formed a monophyletic group, while at other loci, species were intermingled on the phylogeny of alleles. This intermingling probably reflects both incomplete lineage sorting and gene flow after divergence. Likelihood ratio tests rejected a strict allopatric model with no gene flow in comparisons between each pair of species. Gene flow was asymmetric: no gene flow was detected into M. domesticus, while significant gene flow was detected into both M. castaneus and M. musculus. Finally, most of the gene flow occurred at autosomal loci, resulting in a significantly higher ratio of fixed differences to polymorphisms at the X and Y chromosomes relative to autosomes in some comparisons, or just the X chromosome in others, emphasizing the important role of the sex chromosomes in general and the X chromosome in particular in speciation.

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Ecologists need not despair ot discovering the mechanisms that lead to large scale patterns. The search for process at higher scales has already led to enhanced confidence in the patterns and to improvements in their description. For example, species‐area relationships turn out to form not one. but three patterns. Each is controlled by gain‐loss dynamics at its own scale. At the macroscale, origination and global extinction reign. At the archipelagic scale, immigration and island extinction determine the results. At the local scale, metapopulation processes do. The three scales exhibit species‐area curves with systematically different slopes in logarithmic space. We use the three scales of species‐area to illuminate the relationship between local and regional diversity. Algebra shows that the latter pattern is an echo of species‐area curves, and that those echoes ought to be nearly linear. So. we call the relationship of local and regional diversity, the Echo pattern. Ecology has long known that species‐area curves within a region reflect the accumulation of habitat variety. Thus, their connection to Echo patterns argues against concluding that local diversity has little or nothing to do with population interactions. To obtain a pure Echo pattern, one should draw data from independent regions rather than separate islands. The independence allows natural selection to adjust the fundamental niches of species to diversity. Theory suggests that higher diversity should shrink niches, allowing the coexistence of more species locally. Hence, independence should tend to produce the straightest Echoes. However, archipelagic species‐area curves predict that even when different islands are used as the regions, the Echoes should show only very gentle curvatures. Flouting theory, some archipelagic Echoes approach an asymptote as regional diversity increases. These must have logarithmic slopes that increase with regional pool size. We do not understand why.

Aims: (1) Understanding how the relationship between species richness and its determinants depends on the interaction between scales at which the response and explanatory variables are measured. (2) Quantifying the relative contributions of local, intermediate and large‐scale determinants of species richness in a fragmented agro‐ecosystem. (3) Testing the hypothesis that the relative contribution of these determinants varies with the grain size at which species richness is measured. Location: A fragmented agro‐ecosystem in the Southern Judea Lowland, Israel, within a desert–Mediterranean transition zone. Methods: Plant species richness was estimated using hierarchical nested sampling in 81 plots, positioned in 38 natural vegetation patches within an agricultural matrix (mainly wheat fields) among three land units along a sharp precipitation gradient. Explanatory variables included position along that gradient, patch area, patch isolation, habitat heterogeneity and overall plant density. We used general linear models and hierarchical partitioning of variance to test and quantify the effect of each explanatory variable on species richness at four grain sizes (0.0625, 1, 25 and 225 m2). Results: Species richness was mainly affected by position along a precipitation gradient and overall plant density, and to a lesser extent by habitat heterogeneity. It was also significantly affected by patch area and patch isolation, but only for small grain sizes. The contribution of each explanatory variable to explained variance in species richness varied with grain size, i.e. scale‐dependent. The influence of geographic position and habitat heterogeneity on species richness increased with grain size, while the influence of plant density decreased with grain size. Main conclusions: Species richness is determined by the combined effect of several scale‐dependent determinants. Ability to detect an effect and effect size of each determinant varies with the scale (grain size) at which it is measured. The combination of a multi‐factorial approach and multi‐scale sampling reveals that conclusions drawn from studies that ignore these dimensions are restricted and potentially misleading.

Conservation biologists worry that fragmenting a bloc of natural habitat might reduce its species diversity. However, they also recognize the difficulty and importance of isolating the effect of fragmentation from that of simple loss of area. Using two different methods (species-area curve and Fisher's alpha index of diversity) to analyse the species diversities of plants, tenebrionid beetles and carabid beetles in a highly fragmented Mediterranean scrub landscape, we decoupled the effect of degree of fragmentation from that of area loss. In this system, fragmentation by itself seems not to have influenced the number of species. Our results, obtained at the scale of hectares, agree with similar results at island and continent scales.